| adjustment | Access the multiple comparison adjustment method from the... |
| contrastMatrix-class | Class to Contain the Contrast Matrix that Used for Linear... |
| createExpressionSet | Creating an ExpressionSet |
| createGSEAFiles | A Wrapper Function to create *.GCT and *.CLS for GSEA... |
| createIndex | Creating an HTML index file |
| createIngenuityFile | A Wrapper Function to Create Files for Ingenuity Analysis |
| designMatrix-class | Class to Contain the Design Matrix that Used for Linear... |
| eSetExample | An ExpressionSet example |
| exprsExample | a data.frame contains expression data |
| geneFilter | filter an ExpressionSet using different methods |
| getAdjP | access the adjPVal slot from regressResult or... |
| getAnnotation | access the annotation slot from the regressResult or... |
| getCompare1 | Access the Compare1 slot from the contrastMatrix |
| getCompare2 | Access the compare2 slot from the contrastMatrix class |
| getContrast | Access the contrast matrix from the contrastMatrix class |
| getCovariates | Accessing the covariates from the designMatrix class |
| getDesign | Access the design matrix from the designMatrix class |
| getF | access the foldChange slot from regressionResult or... |
| getFC | Access the foldChange slot from the regressResult or... |
| getFCCutoff | Access the significantFCCutoff slot from the regressResult or... |
| getFilterMethod | Access the filterMethod slot from the regressResult or... |
| getID | access the ID slot from the regressResult or... |
| getIndex | Access the SignificantIndex slot from the regressResult or... |
| getInteraction | Access the interaction slot from the contrastMatrix class |
| getIntIndex | Access the IntIndex slot from the designMatrix class |
| getLength | Calculate the Length of interactionResult class |
| getLevel | Access the level slot from the contrastMatrix class |
| getNormalizationMethod | Access the significantIndex slot from the regressResult or... |
| getP | Access the pValue slot from regressResult or... |
| getPCutoff | Access the significantPvalueCutoff slot from regressResult or... |
| getTarget | Access the target slots from the designMatrix class |
| hugene10stCONTROL | hugene10stCONTROL |
| interactionResult-class | Class to Contain the Regression Result Based on An... |
| mogene10stCONTROL | mogene10stCONTROL |
| Output2HTML | Creating HTML file for regressResult or interactionResult... |
| output.cls | Create *.CLS file for GSEA analysis |
| output.gct | Create an *.GCT file for GSEA analysis |
| output.ing | Create an Ingenuity File for Ingenuity Analysis |
| pDataExample | a phenoData example |
| postInteraction | Create an Object of InteractionResult Class for Testing... |
| preProcess3prime | A wrapper function to normalize the the 3 prime array |
| preProcessGeneST | Proprocess genechip ST array |
| qa3prime | Creating Quality Assessment Report for 3 Prime Array |
| qaGeneST | Creating Quality Assessment Report for Gene ST Array |
| QC | sample QC result from Affy Expression Console |
| regress | Run regression to fit genewise linear model |
| regressionMethod | Access the regressionMethod slot from the regressResult or... |
| regressResult-class | Class to Contain the Regression Result |
| selectSigGene | select differentially expressed genes from the regressResult... |
| selectSigGeneInt | select differentially expressed genes from the... |
| Sort | Sort a regressionResult or an interactionResult |
